Chuck vs the Doctor
by HayBales2011
Summary: Chuck and Sarah are finally back on their feet after their fight with Quinn when they are attacked by Daleks. The Daleks are after Chuck's brain, but why? Will Chuck and Sarah, allied with the Doctor and Rose Tyler, be able to put things right? Read on!


Chuck and Sarah Bartowski were having a completely normal day. They had spent the day cooped up in the Castle finishing up paperwork and were almost halfway asleep with boredom when it was finally time to go home. After everything had died down after they defeated Quinn, they spent most of their time restoring Sarah's memory. It didn't take long for it to completely come back, and General Beckman immediately offered them positions in the CIA. They were eager to get back on the spy track. Even though they tried to have a normal life, they realized that they would never actually be normal. Beckman, however, was sending them on less dangerous missions and giving them more safe yet important tasks, like combatting cyber-terrorism, their original plan anyway. They had finished with their paperwork. They were walking up the stairs and had just opened the door to the freezer that hid the entrance to their secret base when they heard a mechanical sort of noise heading towards them. The entered the main shop, and saw three strange-looking mechanical creatures coming right at them. Chuck and Sarah froze in their tracks as the robots advanced on them.

"Exterminate! " A mechanical voice screamed. A blue beam came shooting from one of the robots, aimed right for Sarah. She was able to dodge it, and it hit the wall behind her head. She looked back and there was a black and smoking scorch mark on the wall.

"Run! Back into the Castle!" Sarah yelled, taking Chuck's hand. The three robots started advancing even further on them, all the while screaming and setting off their blue laser beams. Chuck and Sarah dodged and weaved, eventually being able to make their way into the Castle. They quickly closed the door and Sarah bounded down the steps, putting the outside of Castle on full lockdown. They were trapped inside now, but at least they weren't being exterminated.

"What the hell are those things?" Sarah breathed. She looked at her husband and realized that he had no idea where those things had come from either. They jumped when they heard a mechanical voice say from outside:  
"We are Daleks."

The voice was accompanied with several blasts from their laser, almost loud enough to drown out the sound of a blue box materializing right in the middle of the Castle. The presence of said box, however, could not be overlooked, and Sarah drew her gun, having no idea what to make of it. The door opened and out came a normal-looking man wearing a tailored vest and tie and wearing an ankle-length trench coat.

"Oh come on." He said with a British accent, "There's no need for that, I assure you, unless you're an alien intent on destroying the human race." He added.

"Who are you, and why are these things attacking us?" Sarah asked.

"Wow, is this how you usually begin conversations?" The man commented. A young woman with short blonde hair, vaguely resembling Sarah, exited the blue box and stood next to the man.

"You still didn't answer my question." Sarah said.

"I'm the Doctor." He answered, "And this is my friend, Rose Tyler."

"Doctor who?" Sarah asked.

"Nice to meet you, Doctor and Rose Tyler." Chuck said, prompting his wife to drop the gun, "But I guess it's only fair to warn you, we're sort of trapped in here."

"We're not trapped as long as we have the TARDIS." Rose said.

"The…TARDIS?" Chuck asked.

"Long explanation, I'm sorry to say. But I would like to see these things that you say are attacking you." The Doctor said. He walked up the stairs and looked out of the small window of the Castle and saw them.

"They called themselves…Daleks." Sarah said. She noticed the Doctor's eyes grow wide.

"Where are we? When are we?" He asked. Chuck and Sarah looked at each other with stunned looks. What did this man even mean? Who was he?

"Well, It's 2012, and we're in Burbank, California…" Chuck choked out.

"Listen, Doctor, I think you owe us an explanation. What are you and your big blue box doing on government property?" Sarah demanded.

"Government property, eh?" The Doctor said, "And you had a gun which means that you must be…spies. So tell me, are you CIA?"

"Um…yes, we're CIA. I guess we should introduce ourselves. My name is Chuck Bartowski and this is my wife, Sarah."

"Nice to meet you, Mr. and Mrs. Bartowski. Now, if you don't mind, we have real work to do." The Doctor said, "What are Daleks doing in the early 21st century, and on Earth?" The Doctor asked Rose.

"I don't know. Perhaps there's a rift somewhere around here?" She responded.

"No, there's not a rift. I'd sense it if there was one. No, it's something different."

"Excuse me, Doctor, but I'm not finished." Sarah said, "Who are you anyway? And what are these Dalek things?"

"I wasn't aware I had to explain myself to you." Said the Doctor.

"I'm sorry, but as I'm sure you're aware, with your apparent knowledge of everything, as a CIA agent, I don't like being left out of the loop." Sarah said somewhat threateningly.

"If you must know, those _things_ destroyed my planet."

"Your planet?" Chuck questioned, "But wouldn't that be…oh…"

"You're not from around here, then?" Sarah realized.

"No, I'm not. I'm what they call a Time Lord. The TARDIS is essentially a time machine. There used to be billions of us, until the Time War, where the Daleks destroyed our planet, and everyone else along with it. I'm the last one."

"What about her?" Sarah asked, indicating Rose.

"Human, like you guys. I'm from London." Rose responded.

"Well then, I guess we've got introductions out of the way. Now down to business. What would the Daleks be doing around here in a time like this?" The Doctor asked.

"I don't know. Perhaps they're attracted to all the technology in the base? Maybe they need it for something?" Rose wondered.

"If they were attracted to technology, wouldn't they go to a place that specializes in it, like a factory that makes computers or something like that?" Chuck said.

"Or a store that sells them…?" Sarah said.

"I guess there's only one thing to do. Talk to them." The Doctor said.

"You're going to talk to them? You're not afraid of them…you know, exterminating you?" Sarah asked.

"Oh, I'd be the first they'd want to get their hands on." The Doctor said, "But I need to find out where they're from first. I need to make sure they're supposed to be here. If not, I need to set things right and send them back where they came from."

"Supposed to be here?" Chuck said, "You mean that things like that can time travel?"

"It's a very valid possibility, yeah. Back before the war, my people took care of things like this. Now that I'm the last one, I have to take care of all of it myself."

"Sounds lonely." Sarah commented.

"Oh, but he's got me." Rose said, "We're a team, the Doctor and I."

"So are we." Sarah said, taking Chuck's hand.

"Now, let's go see what these things are up to, eh?" The Doctor said, going up the stairs. He looked at the three Daleks standing right outside through the glass. "What are you three doing here? Why here and why now?" He said, loud enough for the Daleks to hear. There was no response. "I order you to answer me, by the 15th Convention of the Shadow Proclamation."

"We will speak to the Doctor." The supposed leader of the group of Daleks said.

"Fantastic." The Doctor said, opening the door. "So, you lot heard what I just said, so answer me."

"We require the brain." The leader of the Daleks said.

"The brain? But what in the universe does that mean?"

"We require the brain." The mechanical voice repeated.

"Well you're just no help at all." The Doctor said, retreating back into the Castle.

"Well what did they say, Doctor?" Rose asked.

"They just said that they need the brain, whatever that is. Maddeningly unhelpful." The Doctor said.

"Well, I suppose we're still stuck here." Sarah said.

"Not really," Rose said, "Doctor, you don't think we could use the TARDIS to get ourselves out of here?"

"Of course we can. I like the way you think, Rose." The Doctor said, "Sarah, is there a way to lock it down so that those things can't get out?" Sarah nodded, and pressed a red button. Sirens started and the shop was sealed off. The Doctor opened the door to the blue police box, "Alright everyone, get in!" He exclaimed. Rose was the first to go through the door, giving a quick smile to the Doctor as she went. Sarah and Chuck looked at each other, then decided to follow Rose into the machine.

"Out of all the odd experiences I've had in my life as a spy, following a strange British man into a time machine that looks like a phone booth definitely takes the cake." Sarah said.

"Actually, Sarah, it's a police box. You know, to phone the police if there's an emergency?" The Doctor said.

"Oh, right, of course, sorry." Sarah said, shooting another glance Chuck's way.

Her mouth gaped open as she stepped into the TARDIS, seeing how large it truly was on the inside.

"I know, right?" Rose commented, "It's bigger on the inside."

"Doctor, I though you said this was a time machine. How would it be able to get us home?" Chuck asked.

"It doesn't have to go through time. It can go through space as well." The Doctor explained.

"Wow, a time machine and a teleportation device all in one…this is like one of those science fiction movies Chuck watches all the time." Sarah said.

"Except this isn't fiction." The Doctor said, adjusting things and pressing buttons, "Here we go." He said as the machine roared to life. The large mechanism in the middle of the ship started to move and make a very distinctive sound that was loud enough for the Daleks to hear from outside the Castle. From the outside, the TARDIS began to disappear, fading until it was entirely gone. Meanwhile, in Chuck and Sarah's apartment, it was starting to appear, materializing bit by bit. The Woodcombs, from their own apartment, could hear the sound.

"What is that?" Ellie asked.

"What is what?" Captain Awesome asked in return.

"That sound, it sounds like it's coming from Chuck and Sarah's place." Ellie said, getting up from the couch where she was nursing baby Clara. She handed the baby to her husband and went over to Sarah and Chuck's apartment, "Chuck, Sarah? Are you there?" She called, knocking on the door. She looked through the window and saw the flashing light of the TARDIS in their living room. "What the heck is that?" She whispered to herself. Ellie let herself in with the spare key that Chuck and Sarah had given her in case of emergencies. The TARDIS was now fully materialized and Chuck and Sarah stepped out, followed by the Doctor and Rose.

"Chuck! Sarah! What the heck is happening here?" Ellie exclaimed.

"Well, El," Chuck began, "I'd like you to meet the Doctor, and his friend Rose. They gave us a lift home. Doctor, Rose, this is my sister, Ellie."

"It's nice to meet you, Ellie." The Doctor said as he shook her hand.

"It's nice to meet you, Doctor…Rose." Ellie said, "What is that thing?" She asked, pointing towards the TARDIS.

"That, my dear lady, is the TARDIS." The Doctor answered.

"It was our ride home." Sarah said with a grin.

"What? But I don't understand…it's just a phone booth!"

"It only looks like a phone box." Rose said, "It can travel through time and space." She said.

"So you guys are some sort of…time travelers?" Ellie asked. Rose and the Doctor both nodded their heads. "But we don't have time machines here, in this time. So, I'm guessing you two aren't from around here?"

"Well, I am. I'm from London." Rose said, "The Doctor, on the other hand…"

"I'm what they call a Time Lord." The Doctor finished.

"You're a…a…an alien?" Ellie said, beginning to feel her pulse race, "And that thing, is some sort of alien thing?"

"What's with you humans and the word 'alien'? It's so harsh…" The Doctor said to Rose.

"Sorry, I'm just a little…startled, that's all." Ellie said, "But why are you guys here?"

"You might want to sit down for this one, El." Chuck said, leading his sister gently to the couch, "When Sarah and I were done with work today, we were coming out of the Castle, and inside the Orange Orange were these robot things. They called themselves Daleks. They tried to attack us."

"Daleks aren't robots, at least not really." The Doctor explained, "It's one of the ugliest beings you've ever seen, like a big glob of goo with tentacles, inside a robotic body."

"Well whatever they are, they tried to kill us." Sarah snapped.

"Oh, they'll do more than try to kill you," The Doctor said, "They won't stop until they exterminate the whole human race. Everything that isn't Dalek. What's worse is that they were made. They were bred to kill, they have no emotions."

"But they said they needed something, the brain." Rose said, "But what could that mean? Ellie, do you have any idea?"

"I might, actually. Chuck, you remember what dad said to you, when he was shot and dying? He said that you were special. Chuck, when I was examining your brain, there was something about it…" Ellie said, "Something's different about your brain Chuck. I mean, it let you carry the Intersect without any ill effects, when it completely destroyed Sarah's memory when she tried to carry it."

"The Intersect? What is that?" Rose asked.

"It's a government program. It's a way of putting information into an agent's brain without them having to learn it. It treats the brain like a computer, and downloads the information onto it. More recently, we were able to put skills into it, such as hand-to-hand combat and..."

"Dancing." Chuck chimed in, "Which I guess in the field can be sort of the same thing."

"The brain as a computer, you say? This is interesting. Ellie, do you still have copies of the scans?" The Doctor asked.

"Well, no, but I can't imagine anything has changed since the first time. I can get us to the hospital. I mean if you think it'll help…"

"You don't think the Daleks might want to use…his brain for something, do you?" Rose asked the Doctor.

"Hard to tell. It'll be easier to know when I know what's special about Chuck's brain."

"Wait a minute, Doctor," Sarah said, "Are you saying that these freaks of nature are after my husband?"

"It definitely seems that way, doesn't it?"

"Then just tell me what to do and I'll do it." Sarah said, "He's risked his own life to save mine plenty of times, it's the least I can do to save his." She said, taking Chuck's hand.

"Now, that's the spirit," said the Doctor, smiling. "Now let's get to the hospital. Allons-y!" He added, following Ellie out of the door. They arrived at the hospital and Ellie used her keycard to get in through the doctor's entrance. The group advanced through the hospital until they were stopped by an old man in a lab coat.

"Dr. Woodcomb, what is going on here?" He asked Ellie. "These guests will need a pass, I'll send you back to security."

"I'm so sorry, sir," The Doctor said, reaching into his pocket, "We're going to be new residents here starting next week, and Dr. Woodcomb was simply showing us around the place. Here's our credentials right here." He said, handing the man a piece of blank paper.

"Ah, right, of course. I'm sorry, sir. Have a good day." The man said, walking away.

"What the heck was that?" Sarah asked, "You just handed him a blank piece of paper and he bought it?"

"That's psychic paper." Rose explained, "It'll show whatever you want to show to anyone you want to show it to. We use it to get into, well, wherever we want."

"Enough chit-chat, ladies, we need to get moving. The longer we wait, the more time the Daleks have to find us." The Doctor said. Ellie led the way into an MRI room and locked the door. She grabbed a hospital gown and motioned for Chuck to put it on. She strapped him into the machine. She pressed a couple of buttons on a computer and it roared to life. Several minutes later, an image popped onto the screen and the Doctor started examining it.

"Wow, now this, this is amazing." The Doctor said as Chuck came back into the exam room, "It's like his brain is made to carry large loads of information. The Daleks must know that somehow, but how?"

"I'm betting they found someone that knew and intimidated it out of them, but who except us would know about it?" Sarah wondered.

"I think I know exactly who." Ellie said. Sarah looked at her in realization.

"You mean…"

"Shaw." Ellie said.

"It's him. It's always him!" Sarah exclaimed.

"It's always who?" Rose asked.

"Daniel Shaw. He was part of our team a couple of years ago, and before I actually started dating Chuck, he kind of came on to me and we started going out. Then he found out that I killed his wife and tried to kill me. Thankfully, Chuck caught onto him and saved me." Sarah explained.

"You…killed his wife?" Rose asked.

"It was a red test, a test all agents have to pass to get their full credentials. As part of it, you have to kill somebody. I was young, and they told me that this woman had defected and was threatening to destroy the CIA. It wasn't until later that I found out that someone had set us up. Someone had tricked the CIA into killing one of our own. It just so happened that the woman that they told me to kill was Shaw's wife, and he ended up working with us. He took me to Paris and he was going to throw me off a bridge into the Seine, but Chuck came and saved me. It ended up with Shaw floating in the Seine with a bullet in his chest and me and Chuck safe back in our hotel room."

"And you think he's the one that told the Daleks about Chuck?" The Doctor asked, "How can he have done that if he's dead?"

"You must see some crazy stuff, Doctor." Chuck said, "People coming back from the dead must be old hat for you. The organization that we had been fighting this entire time, the Ring, apparently was able to fish him out of the river and take him back to their lab and were able to bring up back with something they called cellular regeneration."

"Regeneration, yeah, I'm familiar." The Doctor said, "So he's been tracking you for the past couple of years, then?" He added, and Chuck and Sarah nodded.

"But do you even think that if this Shaw did talk to the Daleks, that he would still be alive?" Rose asked.

"Think about it. Daleks are completely logical, no emotions, except hate. If Shaw had enough leverage against them, enough information to give them, they could have left him alive." The Doctor said.

"No emotions except hate...does that ring a bell?" Sarah asked Chuck.

"We need to find this Shaw and fast. But how?" Rose said.

"We need to get back to the Castle. We can maybe track where he is from there." Sarah said.

"Back to the TARDIS, then. Allons-y!" The Doctor exclaimed, and the group left the hospital and headed back to Chuck and Sarah's apartment. They opened the door and then entered the TARDIS. When Ellie stepped through the doors, her eyes went wide, as anyone else, except the Doctor, who had gone through those doors.

"Yeah, bigger on the inside. I don't have time to explain." The Doctor said, "I have an idea. The Daleks have no need for a brain like Chuck's. They hate everything that isn't Dalek in origin. However, there are some enemies of the Daleks that use the human brain for everything they do."

"The Cybermen." Rose realized.

"Cybermen?" Sarah asked.

"The Cybermen and the Daleks are in constant battle over the planet. I spend most of my time trying to straighten them out. Cybermen are human brains, implanted in a robotic body and deprived of all emotions."

"So you're saying they're human, but not human?" Sarah said.

"And they want my brain…" Chuck said.

"They want to change you into one of them, yes. They probably have plans to make you their king or their leader. I'm sure the Daleks have their own use for you but mainly, the Daleks came to take you simply so that the Cybermen wouldn't be able to have you. An intergalactic war is being fought over the brain of one man. I think you have no idea how important you are at the moment, Charles." The Doctor said.


End file.
